The mitochondrial genome of Phallusia mammillata and Phallusia fumigata (Tunicata, Ascidiacea): High genome plasticity at intra-genus level

BMC Evolutionary Biology

Volumn 7, Issue 1, 2007, Pages

  Iannelli, Fabio ^a   Griggio, Francesca ^a   Pesole, Graziano ^a,b   Gissi, Carmela ^a  

^a UNIVERSITY OF MILAN   (Italy)

^b UNIVERSITY OF BARI   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME B; MITOCHONDRIAL DNA; RIBOSOME RNA; TRANSFER RNA; UNTRANSLATED RNA;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; ASCIDIACEA; CONTROLLED STUDY; GENE ORDER; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOME SIZE; GENUS; MITOCHONDRIAL GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHALLUSIA FUMIGATA; PHALLUSIA MAMMILLATA; RNA STRUCTURE; ANIMAL; CLASSIFICATION; DNA BASE COMPOSITION; GENETICS; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; OPEN READING FRAME; RNA GENE; UROCHORDATA;

ASCIDIA; ASCIDIACEA; ASCIDIIDAE; BRANCHIOSTOMIDAE; CEPHALOCHORDATA; CHORDATA; PHALLUSIA; PHALLUSIA FUMIGATA; PHALLUSIA MAMMILATA; UROCHORDATA; VERTEBRATA;

ANIMALS; BASE COMPOSITION; CYTOCHROMES B; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENE ORDER; GENE REARRANGEMENT; GENES, RRNA; GENOME, MITOCHONDRIAL; OPEN READING FRAMES; RNA, TRANSFER; RNA, UNTRANSLATED; UROCHORDATA;

EID: 38849129515     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-7-155     Document Type: Article

References (75)

1. The use of genome-level characters for phylogenetic reconstruction. JL Boore, Trends Ecol Evol 2006 21 439 446 10.1016/j.tree.2006.05.009 16762445
2. Replication origin of mitochondrial DNA in insects. S Saito K Tamura T Aotsuka, Genetics 2005 171 1695 1705 16118189 10.1534/genetics.105.046243
3. Mapping and characterization of Paracentrotus lividus mitochondrial transcripts: multiple and overlapping transcription units. P Cantatore M Roberti P Loguercio Polosa A Mustich MN Gadaleta, Curr Genet 1990 17 235 245 10.1007/BF00312615 1692770
4. In vitro transcription of human mitochondrial DNA: accurate termination. TW Christianson DA Clayton, Proc Natl Acad Sci USA 1986 83 6277 6281 3018722 10.1073/pnas.83.17.6277
5. Complete mtDNA sequence of the North American freshwater mussel, Lampsilis ornata (Unionidae): an examination of the evolution and phylogenetic utility of mitochondrial genome organization in Bivalvia (Mollusca). JM Serb C Lydeard, Mol Biol Evol 2003 20 1854 1866 10.1093/molbev/msg218 12949150
6. Animal mitochondrial DNA: structure and evolution. DR Wolstenholme, International Rev Cytol 1992 141 173 216
7. Complete sequence of the mitochondrial genome of the tapeworm Hymenolepis diminuta: gene arrangements indicate that Platyhelminths are Eutrochozoans. M von Nickisch-Rosenegk WM Brown JL Boore, Mol Biol Evol 2001 18 721 730 11319256
8. The complete sequences and gene organisation of the mitochondrial genomes of the heterodont bivalves Acanthocardia tuberculata and Hiatella arctica - and the first record for a putative Atpase subunit 8 gene in marine bivalves. H Dreyer G Steiner, Front Zool 2006 3 13 16948842 10.1186/1742-9994-3-13
9. Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAS and has a gene arrangement relatable to those of coelomate metazoans. DV Lavrov WM Brown, Genetics 2001 157 621 637 11156984
10. Nucleotide sequence of cytochrome oxidase (subunit III) from the mitochondrion of the tunicate Pyura stolonifera: evidence that AGR encodes glycine. GA Durrheim VA Corfield EH Harley MH Ricketts, Nucleic Acids Res 1993 21 3587 3588 8393993 10.1093/nar/21.15.3587
11. Changes in mitochondrial genetic codes as phylogenetic characters: two examples from the flatworms. MJ Telford EA Herniou RB Russell DT Littlewood, Proc Natl Acad Sci U S A 2000 97 11359 11364 11027335 10.1073/pnas.97.21.11359
12. Sequence analysis of the mitochondrial genome of Sarcophyton glaucum: conserved gene order among octocorals. MJ Beaton AJ Roger T Cavalier-Smith, J Mol Evol 1998 47 697 708 10.1007/PL00006429 9847412
13. Naked corals: skeleton loss in Scleractinia. M Medina AG Collins TL Takaoka JV Kuehl JL Boore, Proc Natl Acad Sci U S A 2006 103 9096 100. Epub 2006 Jun 5. 16754865 10.1073/pnas.0602444103
14. Mitochondrial genome of the homoscleromorph Oscarella carmela (Porifera, Demospongiae) reveals unexpected complexity in the common ancestor of sponges and other animals. X Wang DV Lavrov, Mol Biol Evol 2007 24 363 373 10.1093/molbev/msl167 17090697
15. Mitochondrial diversity of early-branching metazoa is revealed by the complete mt genome of a haplosclerid demosponge. D Erpenbeck O Voigt M Adamski M Adamska JN Hooper G Worheide BM Degnan, Mol Biol Evol 2007 24 19 22 10.1093/molbev/msl154 17053047
16. Animal mitochondrial genomes. JL Boore, Nucleic Acids Res 1999 27 1767 1780 10101183 10.1093/nar/27.8.1767
17. Evolution of the mitochondrial genome in cephalochordata as inferred from complete nucleotide sequences from two Epigonichthys species. M Nohara M Nishida M Miya T Nishikawa, J Mol Evol 2005 60 526 537 10.1007/s00239-004-0238-x 15883887
18. Mitochondrial genomes of parasitic nematodes-progress and perspectives. M Hu RB Gasser, Trends Parasitol 2006 22 78 84. Epub 2005 Dec 27. 10.1016/j.pt.2005.12.003 16377245
19. Increased rate of gene rearrangement in the mitochondrial genomes of three orders of hemipteroid insects. R Shao NJ Campbell ER Schmidt SC Barker, Mol Biol Evol 2001 18 1828 1832 11504862
20. Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha). ML Thao L Baumann P Baumann, BMC Evol Biol 2004 4 25 15291971 10.1186/1471-2148-4-25
21. Numerous gene rearrangements in the mitochondrial genome of the wallaby louse, Heterodoxus macropus (Phthiraptera). R Shao NJ Campbell SC Barker, Mol Biol Evol 2001 18 858 865 11319269
22. Extraordinary number of gene rearrangements in the mitochondrial genomes of lice (Phthiraptera: Insecta). C Covacin R Shao S Cameron SC Barker, Insect Mol Biol 2006 15 63 68 10.1111/j.1365-2583.2005.00608.x 16469069
23. Genetic characterization of the mitochondrial DNA from Lepeophtheirus salmonis (Crustacea; Copepoda). A new gene organization revealed. K Tjensvoll K Hodneland F Nilsen A Nylund, Gene 2005 353 218 230 10.1016/j.gene.2005.04.033 15987668
24. Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders. RL Mueller JL Boore, Mol Biol Evol 2005 22 2104 2112 10.1093/molbev/msi204 15987876
25. A major mitochondrial gene rearrangement among closely related species. TA Rawlings TM Collins R Bieler, Mol Biol Evol 2001 18 1604 1609 11470854
26. Complete mitochondrial DNA sequence of the eastern oyster Crassostrea virginica. CA Milbury PM Gaffney, Mar Biotechnol (NY) 2005 7 697 712 10.1007/s10126-005-0004-0 16132463
27. The complete maternal and paternal mitochondrial genomes of the Mediterranean mussel Mytilus galloprovincialis: implications for the doubly uniparental inheritance mode of mtDNA. A Mizi E Zouros N Moschonas GC Rodakis, Mol Biol Evol 2005 22 952 967 10.1093/molbev/msi079 15647523
28. Molecular evolution and recombination in gender-associated mitochondrial DNAs of the Manila clam Tapes philippinarum. M Passamonti JL Boore V Scali, Genetics 2003 164 603 611 12807780
29. Molecular mechanisms for the variation of mitochondrial gene content and gene arrangement among chigger mites of the genus Leptotrombidium (Acari: Acariformes). R Shao SC Barker H Mitani M Takahashi M Fukunaga, J Mol Evol 2006 63 251 261 10.1007/s00239-005-0196-y 16830100
30. The complete mitochondrial genomes of Schistosoma haematobium and Schistosoma spindale and the evolutionary history of mitochondrial genome changes among parasitic flatworms. DT Littlewood AE Lockyer BL Webster DA Johnston TH Le, Mol Phylogenet Evol 2006 39 452 467 10.1016/j.ympev.2005.12.012 16464618
31. Phylogenies inferred from mitochondrial gene orders: a cautionary tale from the parasitic flatworms. TH Le D Blair T Agatsuma PF Humair NJ Campbell M Iwagami DT Littlewood B Peacock DA Johnston J Bartley D Rollinson EA Herniou DS Zarlenga DP McManus, Mol Biol Evol 2000 17 1123 1125 10889225
32. Tunicates and not cephalochordates are the closest living relatives of vertebrates. F Delsuc H Brinkmann D Chourrout H Philippe, Nature 2006 439 965 968 10.1038/nature04336 16495997
33. Complete mtDNA of Ciona intestinalis reveals extensive gene rearrangement and the presence of an atp8 and an extra trnM gene in ascidians. C Gissi F Iannelli G Pesole, J Mol Evol 2004 58 376 389 10.1007/s00239-003-2559-6 15114417
34. Mitogenomics reveals two cryptic species in Ciona intestinalis. F Iannelli G Pesole P Sordino C Gissi, Trends Genet 2007 23 9 419 422 10.1016/j.tig.2007.07.001 17640763
35. Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata). S Yokobori T Ueda G Feldmaier-Fuchs S Paabo R Ueshima A Kondow K Nishikawa K Watanabe, Genetics 1999 153 1851 1862 10581290
36. Complete nucleotide sequence of the mitochondrial genome of Doliolum nationalis with implications for evolution of urochordates. S Yokobori T Oshima H Wada, Mol Phylogenet Evol 2005 34 273 283 10.1016/j.ympev.2004.10.002 15619441
37. Mitochondrial genome of Ciona savignyi (Urochordata, Ascidiacea, Enterogona): comparison of gene arrangement and tRNA genes with Halocynthia roretzi mitochondrial genome. S Yokobori Y Watanabe T Oshima, J Mol Evol 2003 57 574 587 10.1007/s00239-003-2511-9 14738316
38. Transcript Mapping and Genome Annotation of Ascidian mtDNA Using EST Data. C Gissi G Pesole, Genome Res 2003 13 2203 2212 12915488 10.1101/gr.1227803
39. Rare genomic changes as a tool for phylogenetics. A Rokas PW Holland, Trends Ecol Evol 2000 15 454 459 10.1016/S0169-5347(00)01967-4 11050348
40. Tandem duplication of D-loop and ribosomal RNA sequences in lizard mitochondrial DNA. C Moritz WM Brown, Science 1986 233 1425 1427 10.1126/science.3018925 3018925
41. The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals. JL Boore, Comparative Genomics Dordrech/Boston/London, Kluwer Academic, Sankoff D and Nadeau JH, Computational Biology. 2000 1 133 147
42. Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss. DV Lavrov JL Boore WM Brown, Mol Biol Evol 2002 19 163 169 11801744
43. Animal mitochondrial DNA recombination. DH Lunt BC Hyman, Nature 1997 387 247 10.1038/387247a0 9153388
44. Novel mitochondrial gene content and gene arrangement indicate illegitimate inter-mtDNA recombination in the chigger mite, Leptotrombidium pallidum. R Shao H Mitani SC Barker M Takahashi M Fukunaga, J Mol Evol 2005 60 764 773 10.1007/s00239-004-0226-1 15931495
45. The relationship between the rate of molecular evolution and the rate of genome rearrangement in animal mitochondrial genomes. W Xu D Jameson B Tang PG Higgs, J Mol Evol 2006 63 3 375 392 10.1007/s00239-005-0246-5 16838214
46. tRNA punctuation model of RNA processing in human mitochondria. D Ojala J Montoya G Attardi, Nature 1981 290 470 474 10.1038/290470a0 7219536
47. Complete mitochondrial genome sequence of the polychaete annelid Platynereis dumerilii. JL Boore, Mol Biol Evol 2001 18 1413 1416 11420379
48. Evolutionary conservation of protein regions in the protonmotive cytochrome b and their possible roles in redox catalysis. N Howell, J Mol Evol 1989 29 157 169 10.1007/BF02100114 2509716
49. Evolution of the cytochrome b gene of mammals. DM Irwin TD Kocher AC Wilson, J Mol Evol 1991 32 128 144 10.1007/BF02515385 1901092
50. Mitochondrial cytochrome b: evolution and structure of the protein. M Degli Esposti S De Vries M Crimi A Ghelli T Patarnello A Meyer, Biochim Biophys Acta 1993 1143 243 271 10.1016/0005-2728(93)90197-N 8329437
51. Mutational analysis of the mouse mitochondrial cytochrome b gene. N Howell K Gilbert, J Mol Biol 1988 203 607 618 10.1016/0022-2836(88)90195-7 3210228
52. Estimating the influence of selection on the variable amino acid sites of the cytochrome B protein functional domains. DA McClellan KG McCracken, Mol Biol Evol 2001 18 917 925 11371579
53. The mitochondrial genomes of the human hookworms, Ancylostoma duodenale and Necator americanus (Nematoda: Secernentea). M Hu NB Chilton RB Gasser, Int J Parasitol 2002 32 145 158 10.1016/S0020-7519(01)00316-2 11812491
54. RNA editing changes the identity of a mitochondrial tRNA in marsupials. GV Borner M Morl A Janke S Paabo, Embo J 1996 15 5949 5957 8918472
55. Evidence for import of a lysyl-tRNA into marsupial mitochondria. M Dorner M Altmann S Paabo M Morl, Mol Biol Cell 2001 12 2688 2698 11553708
56. Editing of a tRNA anticodon in marsupial mitochondria changes its codon recognition. A Janke S Paabo, Nucleic Acids Res 1993 21 1523 1525 8479901 10.1093/nar/21.7.1523
57. Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. Y Kumazawa M Nishida, J Mol Evol 1993 37 380 398 10.1007/BF00178868 7508516
58. Evolution and phylogenetic information content of mitochondrial genomic structural features illustrated with acrodont lizards. JR Macey JA Schulte 2nd A Larson, Syst Biol 2000 49 257 277 10.1080/10635159950173843 12118408
59. Evolution of the WANCY region in amniote mitochondrial DNA. G Seutin BF Lang DP Mindell R Morais, Mol Biol Evol 1994 11 329 340 8015429
60. The mitochondrial genomes of soft ticks have an arrangement of genes that has remained unchanged for over 400 million years. R Shao Y Aoki H Mitani N Tabuchi SC Barker M Fukunaga, Insect Mol Biol 2004 13 219 224 10.1111/j.0962-1075.2004.00447.x 15157222
61. The novel mitochondrial gene arrangement of the cattle tick, Boophilus microplus: fivefold tandem repetition of a coding region. NJ Campbell SC Barker, Mol Biol Evol 1999 16 732 740 10368952
62. The mitochondrial genomes of Campodea fragilis and Campodea lubbocki (Hexapoda: Diplura): High genetic divergence in a morphologically uniform taxon. L Podsiadlowski A Carapelli F Nardi R Dallai M Koch JL Boore F Frati, Gene 2006 381 49 61 10.1016/j.gene.2006.06.009 16919404
63. Transfer RNA gene recruitment in mitochondrial DNA. DV Lavrov BF Lang, Trends Genet 2005 21 129 133 10.1016/j.tig.2005.01.004 15734570
64. Changing identities: tRNA duplication and remolding within animal mitochondrial genomes. TA Rawlings TM Collins R Bieler, Proc Natl Acad Sci U S A 2003 100 15700 15705 14673095 10.1073/pnas.2535036100
65. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. TM Lowe SR Eddy, Nucleic Acids Res 1997 25 955 964 9023104 10.1093/nar/25.5.955
66. PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance. G Pesole S Liuni M D'Souza, Bioinformatics 2000 16 439 450 10.1093/bioinformatics/ 16.5.439 10871266
67. A backtranslation method based on codon usage strategy. G Pesole M Attimonelli S Liuni, Nucleic Acids Res 1988 16 1715 1728 3281142 10.1093/nar/16.5.1715
68. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. NT Perna TD Kocher, J Mol Evol 1995 41 353 358 10.1007/BF01215182 7563121
69. REPuter: the manifold applications of repeat analysis on a genomic scale. S Kurtz JV Choudhuri E Ohlebusch C Schleiermacher J Stoye R Giegerich, Nucleic Acids Res 2001 29 4633 4642 11713313 10.1093/nar/29.22.4633
70. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson, Nucleic Acids Res 1994 22 4673 4680 7984417 10.1093/nar/22.22.4673
71. GeneSyn: a tool for detecting conserved gene order across genomes. G Pavesi G Mauri F Iannelli C Gissi G Pesole, Bioinformatics 2004 20 1472 4. Epub 2004 Feb 19. 10.1093/bioinformatics/bth102 14976031
72. Breakpoint Phylogenies. M Blanchette G Bourque D Sankoff, Genome Inform Ser Workshop Genome Inform 1997 8 25 34 11072302
73. A codon-based model of nucleotide substitution for protein-coding DNA sequences. N Goldman Z Yang, Mol Biol Evol 1994 11 725 736 7968486
74. PAML: a program package for phylogenetic analysis by maximum likelihood. Z Yang, Comput Appl Biosci 1997 13 555 556 9367129
75. Influence of base composition on quantitative estimates of gene evolution. C Saccone C Lanave G Pesole G Preparata, Methods Enzymol 1990 183 570 583 2156131